getLocOrfs               package:ScISI               R Documentation

_A _f_u_n_c_t_i_o_n _t_o _o_b_t_a_i_n _O_R_F_s _f_o_r _t_h_e _S_c_I_S_I

_D_e_s_c_r_i_p_t_i_o_n:

     This function takes a list of bi-partite graph incidence matrices
     as well as a vector of GO nodes, and for each protein complex of
     each bi-partite graph, finds those constituent member proteins
     which are annotated to each GO node.

_U_s_a_g_e:

     getLocOrfs(imList, goNode, pathToSave = NULL, name = NULL)

_A_r_g_u_m_e_n_t_s:

  imList: A list of bi-partite graph incidence matrices

  goNode: A character vector of GO ID's

pathToSave: A character denoting where to save the resultant data

    name: The name by which the resulting R-object as well as the file
          will be named

_D_e_t_a_i_l_s:

     Currently, this function will take a protein complex and find
     those constituent protein members which have also been annotated
     to the user specified GO ID. For instance, the GO ID "" is the
     nucleus ID. This function will find all proteins within an
     interactome which has been annotated with the ID "". NB - if n GO
     ID is supplied, the function returns n different interactomes,
     each is has proteins uniquely annotated with each GO ID.

_V_a_l_u_e:

     The return value is a list of lists of lists:

     1. The top level list contains entries named by each GO ID 2. The
     second tier level contains entries after each entry of imList 3.
     The third tier level contains three entries: i.   A bi-partite
     graph incidence matrix which only has protein complexes restricted
     to the respective GO ID annotation ii.  A bi-partite graph
     incidence matrix which only has protein complexes listed in (i)
     but contains all the original proteins iii. A vector of
     proportions. We look at the column sums of (i) divided by the
     column sums fo (ii). This gives the ratio of proteins which are
     annotated by the GO ID over all other proteins in that complex    

restrictedOrfsComp: A bi-partite graph incidence matrix which only has
          protein complexes restricted to the respective GO ID
          annotation

restrictedOrfsOnly: A bi-partite graph incidence matrix which only has
          protein complexes listed in (i) but contains all the original
          proteins

   ratio: A vector of proportions. We look at the column sums of (i)
          divided by the column sums fo (ii). This gives the ratio of
          proteins which are annotated by the GO ID over all other
          proteins in that complex

_A_u_t_h_o_r(_s):

     TC

_R_e_f_e_r_e_n_c_e_s:

     ~put references to the literature/web site here ~

